Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF (PPG)4-OVG-(PPG)4, MONOCLINIC, TWINNED CRYSTAL
 
Authors :  K. Okuyama, T. Morimoto, K. Mizuno, H. P. Bachinger
Date :  21 Mar 09  (Deposition) - 02 Mar 10  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.02
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Collagen, Triple-Helix, Model Peptide, Twinned Crystal, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Okuyama, K. Miyama, T. Morimoto, K. Masakiyo, K. Mizuno, H. P. Bachinger
Stabilization Of Triple-Helical Structures Of Collagen Peptides Containing A Hyp-Thr-Gly, Hyp-Val-Gly, Or Hyp-Ser-Gly Sequence.
Biopolymers V. 95 628 2011
PubMed-ID: 21442606  |  Reference-DOI: 10.1002/BIP.21625

(-) Compounds

Molecule 1 - COLLAGEN-LIKE PEPTIDE
    Chains: A, B, C, D, E, F
    Engineered: YES
    Other Details: THIS PEPTIDE WAS CHEMICALLY SYSTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1HYP7Mod. Amino Acid4-HYDROXYPROLINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1HYP3Mod. Amino Acid4-HYDROXYPROLINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1HYP4Mod. Amino Acid4-HYDROXYPROLINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY D:15 , VAL E:14 , GLY E:15 , GLY F:15 , PRO F:16 , PRO F:17 , GLY F:18 , HOH F:266 , HOH F:339 , HOH F:353BINDING SITE FOR RESIDUE PRO F 16

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A0M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A0M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A0M)

(-) Exons   (0, 0)

(no "Exon" information available for 3A0M)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:26
                                                         
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author .......................... Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                  3a0m A  1 PPGPPGPPGPPGpVGPPGPPGPPGPP 26
                                    10  |     20      
                                       13-HYP         


Chain B from PDB  Type:PROTEIN  Length:24
                                                       
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ........................ Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                  3a0m B  4 PPGPPGPPGpVGPPGPPGPPGPPG 27
                                    13        23    
                                    13-HYP          


Chain C from PDB  Type:PROTEIN  Length:25
                                                        
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ......................... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  3a0m C  3 GPPGPPGPPGpVGPPGPPGPPGPPG 27
                                    12|       22     
                                     13-HYP          


Chain D from PDB  Type:PROTEIN  Length:24
                                                       
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ........................ Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                  3a0m D  3 GPPGPPGPPGpVGPPGPPGPPGPP 26
                                    12|       22    
                                     13-HYP         


Chain E from PDB  Type:PROTEIN  Length:25
                                                        
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ......................... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  3a0m E  1 PPGPPGPPGPPGpVGPPGPPGPPGP 25
                                    10  |     20     
                                       13-HYP        


Chain F from PDB  Type:PROTEIN  Length:28
                                                           
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author ............................ Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                  3a0m F  4 PPGPPGPPGpPVPGPpPVGPPGPPGPPG 27
                                    13     |  19        
                                    13-HYP |            
                                          16-HYP
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3A0M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A0M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A0M)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3A0M)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    HYP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3a0m)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3a0m
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3A0M)

(-) Related Entries Specified in the PDB File

2cuo THE SIMILAR COLLAGEN-LIKE PEPTIDE
3a08 THE SIMILAR HOST-GUEST PEPTIDE
3a0a THE SIMILAR HOST-GUEST PEPTIDE